Specialized transducing bacteriophage lambda carrying the structural gene for a major outer membrane matrix protein of Escherichia coli K-12

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Domains involved in osmoregulation of the ompF gene in Escherichia coli

Expression of the ompF gene, which is under the control of the OmpR protein, is regulated by the osmolarity of the medium. To study the mechanism of osmoregulation, plasmids carrying two different types of chimeric genes were constructed. In one type, the coding region of the ompF gene was linked to the trp promoter (trpPO) preceding ompF, and in the other type the ompF upstream region, mostly composed of the region for regulation by OmpR and the promoter region, was linked to the lacZ gene by protein fusion. Expression of beta-galactosidase by the lacZ chimeric gene was OmpR dependent and osmoregulated as sensitively as that of the intact ompF gene. In the ompR20 background the direction of osmoregulation was opposite that of normal osmoregulation, as was the direction of osmoregulation of the intact ompF gene. Osmoregulation was also observed with trpPO-ompF chimeric genes. However, the regulation was not as sensitive to the osmolarity of the medium as was regulation of the intact ompF gene and was independent of OmpR. These results suggest that OmpR-dependent osmoregulation played a primary role in the osmoregulation of ompF expression and that ompR-independent osmoregulation most likely did not play a crucial role. Studies with a series of trpPO-ompF chimeric genes also suggest that the untranslated leader region, about 100 base pairs in length, between the transcription initiation site and the initiation codon was not required for osmoregulation.

Primary characterization of the protein products of the Escherichia coli ompB locus: structure and regulation of synthesis of the OmpR and EnvZ proteins

The ompB operon of Escherichia coli contains the structural genes for two proteins, OmpR and EnvZ, which control the osmoregulated biosynthesis of the porin proteins OmpF and OmpC. By inserting XbaI octamer linkers into the cloned ompB locus, four distinct frameshift mutants were isolated and subsequently characterized for their OmpR and EnvZ protein products and their outer membrane porin phenotype. In a minicell expression system, the wild-type products of the ompR and envZ genes were found to be approximately 28 and 50 kilodaltons in size, respectively, whereas the mutant proteins were either truncated or extended due to the frame shift. The identity of the envZ gene product was confirmed by immunoprecipitation. M13 dideoxy sequencing of the DNA around the wild-type ompR-envZ junction revealed an error in the sequence published for this operon; the complete corrected sequence is presented. A sequence, ATGA, was found that forms the termination codon for the OmpR reading frame and a possible initiation codon for the EnvZ protein; these sequences are consistent with the sizes of the proteins observed after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The translational activity of this ATG codon was confirmed by fusing the lacZ gene in frame with the putative EnvZ coding sequence. The implications of these results are discussed with respect to the regulation of synthesis of the ompB gene products.

Positive control of transcription initiation in Escherichia coli. A base substitution at the Pribnow box renders ompF expression independent of a positive regulator

Expression of the ompF gene coding for a major outer membrane protein of Escherichia coli is positively regulated by the product of the ompR gene, OmpR. Using an ompF-tet chimera gene, ompF promoter mutants that render the ompF expression independent of the OmpR protein were isolated. In all of the four mutants that were isolated separately, the first base of the Pribnow box was changed from A to T. The mutant promoter did not require the upstream domain of the -35 region that is required for the OmpR-dependent functioning of the wild-type promoter. It is concluded that the domain upstream from the -35 region plays a role in the positive regulation by the OmpR protein. A statistical survey of the E. coli promoter sequence revealed that almost all of the genes that do not require an activator protein for their expression possess T at the first position of the Pribnow box, while the position is occupied by other bases in almost all of the positively regulated genes. Based on these facts, the mechanism of positive regulation of the gene expression by an activator protein is discussed.

Construction and characterization of a deletion mutant lacking micF, a proposed regulatory gene for OmpF synthesis in Escherichia coli

A method is presented for the construction of a deletion mutant lacking the micF gene, which has been proposed to negatively regulate expression of the ompF gene. The method includes (i) construction of a temperature-sensitive plasmid containing a chromosomal fragment that carries both flanking regions of the micF gene but does not carry micF itself and (ii) replacement of the corresponding chromosomal domain with the fragment. The method is applicable to construction of a deletion mutant for any Escherichia coli chromosomal gene provided that it is dispensable. The micF deletion was confirmed by genetic and biochemical tests, including nucleotide sequence analysis. ompF expression in the micF deletion mutant thus constructed was normally regulated and was not enhanced. When micF was cloned into a high-copy-number plasmid it repressed ompF gene expression, whereas when cloned into a low-copy-number plasmid it did not. From these results, it is concluded that a single copy of the micF gene on the E. coli chromosome does not play a critical role in ompF gene expression.

Gene encoding a hybrid OmpF--PhoE pore protein in the outer membrane of Escherichia coli K12

To study the structure-function relationship of outer membrane pore proteins of E. coli K12, a hybrid gene was constructed in which the DNA encoding amino acid residues 2-73 of the mature PhoE protein is replaced by the homologous part of the related ompF gene. The product of this gene is incorporated normally into the outer membrane. It was characterized with respect to its pore activity and its phage receptor and colicin receptor properties. It is concluded that the preference of the PhoE protein pore for negatively charged solutes is partly determined by the amino terminal 73 amino acids, that part of the receptor site of PhoE protein for phage TC45 is located in this part of the protein, that colicin N uses OmpF protein as (part of) its receptor, that the specificity of OmpF protein as a colicin N receptor is completely located within the 80 amino terminal amino acid residues, whereas the specificity of this protein as a colicin A receptor is completely located within the 260 carboxy terminal amino acid residues, and that the amino terminal 73 amino acid residues of PhoE protein span the membrane at least once.

Promoter exchange between ompF and ompC, genes for osmoregulated major outer membrane proteins of Escherichia coli K-12

Expression of the ompF and ompC genes coding for major outer membrane proteins OmpF and OmpC is regulated in opposite directions by medium osmolarity. Chimera genes were constructed by a reciprocal exchange of the promoter-signal sequence region between the two genes. The chimera gene construction was designed so that the proteins synthesized by these genes were essentially the same as the OmpC and OmpF proteins. Studies with the chimera genes demonstrated that the osmoregulation of the OmpF-OmpC synthesis was promoter dependent. They also showed that cells grew normally even when the osmoregulation took place in opposite directions. The effects of the ompR2 and envZ mutations, which suppress ompC and ompF expression, respectively, also became reversed. The reduced expression was still subject to the promoter-controlled osmoregulation. Based on these observations, the mechanism of regulation of the ompF-ompC gene expression and its physiological importance are discussed.

Mutation causing overproduction of outer membrane protein OmpF and suppression of OmpC synthesis in Escherichia coli

A novel mutation affecting the synthesis of major outer membrane proteins OmpF and OmpC in Escherichia coli K-12 is described. The mutation resulted in overproduction of the OmpF protein with concomitant suppression of OmpC synthesis. This mutation, designated as ompFp100, was mapped at 21 min on the E. coli chromosome map with the gene order aroA-aspC-ompF4-ompFp100-asnS-pyrD. This mutation was cis-dominant to the expression of the ompF gene. In addition, the direction of the mRNA transcription of the ompF gene was from asnS to aspC. These results strongly indicate that ompFp100 is a promoter mutation of the ompF gene. Introduction of an ompF mutation, which causes the disappearance of the OmpF protein, into strains carrying the ompFp100 mutation resulted in the reappearance of the OmpC protein in the outer membrane. Addition of a high concentration of sucrose to the medium, which suppresses the OmpF synthesis and stimulates the OmpC synthesis in the wild-type strain, resulted in the reappearance of the OmpC protein in the ompFp100 mutant with concomitant suppression of the overproduction of the OmpF protein. These results suggest that suppression of OmpC synthesis in the ompFp100 mutant is due to overproduction of the OmpF protein.

Regulation of outer membrane porin protein synthesis in Escherichia coli K-12: ompF regulates the expression of ompC

The relative amounts of the OmpF and OmpC proteins in the outer membrane of Escherichia coli K-12 are affected differentially by high concentrations of substances like sucrose in culture media in such a manner that a decrease in the amount of the OmpF protein appears to be compensated for by a reciprocal increase in the OmpC protein. When an ompF mutation was introduced, OmpC synthesis became almost independent of sucrose and occurred at the fully induced level even in the absence of sucrose. On the other hand, introduction of an ompC mutation did not affect the sucrose-dependent profile of OmpF synthesis. The effect of the ompF mutation was also examined with the ompC-lac fusion strain, in which expression of beta-galactosidase is under the control of the ompC promoter. The expression of beta-galactosidase coded for by the ompC-lac fusion in the ompF+ and ompF- strains was essentially the same as that of the OmpC protein, being sucrose dependent in the ompF+ strain and sucrose-independent in the ompF mutant. From these results we conclude that sucrose in the medium primarily regulates ompF gene expression, which in turn regulates ompC gene expression at the transcriptional level. This sequential regulatory mechanism is discussed in relation to the function of the ompB locus.

Primary structure of the ompF gene that codes for a major outer membrane protein of Escherichia coli K-12

The nucleotide sequence of the ompF gene coding for a major outer membrane protein of Escherichia coli K-12 has been determined and the amino acid sequence of the OmpF protein was deduced from it. The OmpF protein contains 340 amino acid residues, and is produced from a precursor having 22 extra amino acid residues, the signal peptide, at the amino terminus. The expected secondary structure of the OmpF protein had a high beta-sheet content with a low alpha-helix content. The promoter region and the transcription termination region of the ompF gene had a significantly high AT content, while the AT content of the coding region was about the same as the average AT content of the E. coli chromosome. Following the termination codon, a typical rho-independent transcription termination signal was observed. The codon usage in the ompF gene was highly nonrandom; the codons preferably utilized are those recognized by the most abundant species of isoaccepting tRNAs or those, among synonymous codons recognized by the same tRNA, that can interact more properly with the anticodon.

Roles of lipopolysaccharide and outer membrane protein OmpC of Escherichia coli K-12 in the receptor function for bacteriophage T4

The roles of lipopolysaccharide and OmpC, a major outer membrane protein, in the receptor function for bacteriophage T4 were studied by using Escherichia coli K-12 strains having mutations in the ompC gene or in genes controlling different stages of lipopolysaccharide synthesis. The receptor activity for T4 was monitored by (i) T4 sensitivity of intact cells, (ii) phage inactivation activity of cell envelopes, and (iii) phage inactivation activity of specimens reconstituted from purified OmpC and lipopolysaccharide. It was found that (i) in the presence of the OmpC protein, the essential region of the lipopolysaccharide for the receptor activity was the core-lipid A region that includes the heptose region, whereas the glucose region was not necessarily required for the receptor function; (ii) the OmpC protein was not required at all when the distal end of the lipopolysaccharide was removed to expose a glucose residue at the distal end; and (iii) when cells lacked both the OmpC protein and the glucose region, they became extremely resistant to T4. Based on these findings, the roles of the OmpC protein and lipopolysaccharide in T4 infection are discussed.

The tolC locus of Escherichia coli affects the expression of three major outer membrane proteins

tolC mutants, which are resistant to colicin E1 and also highly sensitive to detergents and dyes, were shown to lack the OmpF outer membrane protein. There was little effect on transcription as judged by the use of an ompF-lac operon fusion strain, and the tolC effect was probably due to a post-transcriptional effect. The NmpC protein and protein 2 were also tolC dependent.

Genetic and biochemical characterization of an Escherichia coli K-12 mutant with an altered outer membrane protein

The properties of an Escherichia coli K-12 mutant are described which seemingly produces a "new" major outer membrane protein with an apparent molecular weight of 40 000. This 40K protein was purified and its cyanogen bromide (CNBr) fragments were compared with those of several known major outer membrane proteins. A similarity was found between the CNBr fragments of the 40K protein and those of the OmpF protein (molecular weight 37 000). In addition, the 40K protein was found to be regulated exactly like the OmpF protein, and the mutation which causes the production of the 40K protein has been localized in (or very close to) the ompF gene. It is concluded that the 40K protein is a mutant form of the OmpF protein. The results provide additional evidence that the ompF gene at minute 21 is the structural gene for the OmpF protein.